Access spatial analysis results

Read the cluster assignments, parameters, and summary for a spatial method from a Seurat object's stored tool result. If detailed results were not stored, cluster assignments are read from the corresponding metadata column. BANKSY retains a lightweight index for custom result columns and exact sample membership. Sample retrieval requires this index or stored per-sample results; sample identity is never inferred from cluster labels.

Results describe cells present in object, in its current cell order, rather than the original fit's full cell set. BANKSY domain counts and PRECAST cell, domain, and sample counts are recomputed from the returned assignments. Unfitted PRECAST cells are excluded. Parameters and the native bundles in object@tools still describe the original fit; other methods' stored summaries are omitted when their cell set changes. PRECAST can be selected by its tool name or by "PRECAST" when that method identifies a unique stored bundle.

New BANKSY fits and detailed SmoothClust, CHOIR, RareQ, and PRECAST results retain a private metadata identity column, named by the result index. Preserve this column to retrieve results after subset() or RenameCells(); names are mapped by saved identities, never by order or sample prefixes. Missing, duplicate, or unknown identities cause an informative error. SmoothClust and CHOIR's explicit cell columns also reflect the current IDs. Legacy saved assignments support exact-ID subsets. Contradictory metadata causes an error, but renames cannot always be detected without provenance; rerun the method to establish identity tracking. Legacy PRECAST and metadata-only results use their current metadata assignments.

Storage-disabled methods other than BANKSY retain their existing storage behavior. Custom metadata columns require a stored locator; the accessor does not guess a column from its values or prefix.

Usage

GetSpatialResult(object, method, sample = NULL)

Arguments

object

A Seurat object returned by a spatial method.

method

Name of the method or tool entry, such as "BANKSY".

sample

Optional BANKSY sample label, or a sample label for another method that stored per-sample results.

Value

A list with clusters, parameters, and summary. Values that were not stored by the method are returned as NULL; BANKSY and PRECAST summaries are recomputed from the returned cluster assignments, including empty results.

Examples

data(visium_human_pancreas_sub)
if (FALSE) { # \dontrun{
spatial <- RunBANKSY(
  visium_human_pancreas_sub,
  layer = "counts",
  features = rownames(visium_human_pancreas_sub)[1:200],
  verbose = FALSE
)
GetSpatialResult(spatial, "BANKSY")
} # }